3I5R

PI3K SH3 domain in complex with a peptide ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural studies of the phosphatidylinositol 3-kinase (PI3K) SH3 domain in complex with a peptide ligand: role of the anchor residue in ligand binding.

Batra-Safferling, R.Granzin, J.Modder, S.Hoffmann, S.Willbold, D.

(2010) Biol.Chem. 391: 33-42

  • DOI: 10.1515/BC.2010.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Src homology 3 (SH3) domains are mediators of protein-protein interactions. They comprise approximately 60 amino acid residues and are found in many intracellular signaling proteins. Here, we present the crystal structure of the SH3 domain from phosp ...

    Src homology 3 (SH3) domains are mediators of protein-protein interactions. They comprise approximately 60 amino acid residues and are found in many intracellular signaling proteins. Here, we present the crystal structure of the SH3 domain from phosphatidylinositol 3-kinase (PI3K) in complex with the 12-residue proline-rich peptide PD1R (HSKRPLPPLPSL). The crystal structure of the PI3K SH3-PD1R complex at a resolution of 1.7 A reveals type I ligand orientation of the bound peptide with an extended conformation where the central portion forms a left-handed type II polyproline (PPII) helix. The overall structure of the SH3 domain shows minimal changes on ligand binding. In addition, we also attempted crystallization with another peptide ligand (PD1) where the residue at anchor position P(-3) is a tyrosine. The crystals obtained did not contain the PD1 ligand; instead, the ligand binding site is partially occupied by residues Arg18 and Trp55 from the symmetry-related PI3K SH3 molecule. Considering these crystal structures of PI3K SH3 together with published reports, we provide a comparative analysis of protein-ligand interactions that has helped us identify the individual residues which play an important role in defining target specificity.


    Organizational Affiliation

    Institut für Strukturbiologie und Biophysik ISB-2, Forschungszentrum Jülich, D-52425 Jülich, Germany. r.batra-safferling@fz-juelich.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alpha
A
83Homo sapiensMutation(s): 0 
Gene Names: PIK3R1 (GRB1)
Find proteins for P27986 (Homo sapiens)
Go to Gene View: PIK3R1
Go to UniProtKB:  P27986
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide ligand
B
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.365α = 90.00
b = 60.365β = 90.00
c = 46.525γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
ADSCdata collection
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance